amplicR: amplicR
In carlopacioni/amplicR: An R package to process amplicon data
amplicR R Documentation
amplicR
Description
An R package to process amplicon data.
Details
This package has a number of functions to filter, dereplicate and error and
chimera check NGS
reads stored in fastq files. This funcitonality is currently limted to
single-read analysis. The retained reads after the data processing described
above (or your own reads if you have done
this already in another way) can then be compared against reference sequences
and the number of mismatch is reported. This may be useful when, for example,
screening samples for particular taxa (e.g. a pathogen).
amplicR is mainly a wrapper of several functions provided by other R
packages in order to automate some common analyses, so if you use it, please
make sure to also cite the relevant packages (these are generally indicated
in the documentation of amplicR's functions). To find out the correct
citation for a package, you can use the function:
citation("package_name") where you have to replace package_name with
the actual name of the package you are interested into.
Documentations
Use help(package = "amplicR") for a list of
amplicR functions and their specific documentations.
A more detailed description of the package and functions can be opened
with:
vignette(package="amplicR", topic="amplicR-package")
- This is pending... hang in there
Citation
If you use amplicR, please cite:
This is also pending
Get in touch
Please, use
https://github.com/carlopacioni/amplicR/issues to report any issues
with amplicR. If unsure, or for feedback, contact me at:
carlo.pacioni 'at' gmail.com.
carlopacioni/amplicR documentation built on Aug. 19, 2023, 7:59 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| amplicR | R Documentation |
amplicR
Description
An R package to process amplicon data.
Details
This package has a number of functions to filter, dereplicate and error and chimera check NGS reads stored in fastq files. This funcitonality is currently limted to single-read analysis. The retained reads after the data processing described above (or your own reads if you have done this already in another way) can then be compared against reference sequences and the number of mismatch is reported. This may be useful when, for example, screening samples for particular taxa (e.g. a pathogen).
amplicR is mainly a wrapper of several functions provided by other R
packages in order to automate some common analyses, so if you use it, please
make sure to also cite the relevant packages (these are generally indicated
in the documentation of amplicR's functions). To find out the correct
citation for a package, you can use the function:
citation("package_name") where you have to replace package_name with
the actual name of the package you are interested into.
Documentations
Use help(package = "amplicR") for a list of
amplicR functions and their specific documentations.
A more detailed description of the package and functions can be opened with:
vignette(package="amplicR", topic="amplicR-package")
- This is pending... hang in there
Citation
If you use amplicR, please cite:
This is also pending
Get in touch
Please, use
https://github.com/carlopacioni/amplicR/issues to report any issues
with amplicR. If unsure, or for feedback, contact me at:
carlo.pacioni 'at' gmail.com.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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